隐马尔可夫模型
隐马尔可夫链模型 Hidden Markov Model
首先应当了解马尔科夫链模型，隐马尔可夫链模型即可以解决马尔可夫链模型状态量非常多的情况下（如 连续值）转移矩阵过大的问题，并由它转化而来。解决原理是假定当前状态（称为显状态）仅由隐状态决定，由于隐状态可以比当前状态少很多，因此转移矩阵参数更少。
隐马尔可夫模型的分类：离散、连续。
隐马尔可夫模型的典型功能
- 根据一个或多个已知的可见层和隐藏层训练模型，获得释放矩阵和状态转移矩阵，得到模型参数。
- 使用前向算法、后向算法或者暴力算法，根据已知模型的参数，求出某一已知可见层序列的发生概率。
- 使用维特比（Viterbi）算法根据一个可见层序列推导出最有可能的隐藏层序列。
python实现
此处利用python对离散的隐马尔可夫模型进行建模，满足其训练、计算和推导的功能。
由于篇幅限制，本篇仅实现其前向算法、后向算法、遍历（暴力）算法的实现，和相关准备工作
下面是hmm类本体get_prob实现典型功能2的功能，而fit在本章中使用具有隐藏层和可见层的数据进行计算，而Baum-Welch算法和Viterbi算法在后续篇幅进行介绍，本类对相关算法部分留下了篇幅
#hmm.py
from operator import truediv
import numpy as np
class discrete_hidden_Markov_model:
def __init__(self, debug:bool=False):
#typical 5 model params of hmm(lambda(Pi, A, B))
self.vis_kind = None
self.invis_kind = None
self.init_state_mat = None
self.trans_state_mat = None
self.emitter_mat = None
#configurations
self.debug = debug
#from a visible chain, or a visible chain with an invisible chain, infer the params of the hmm model
def fit(self, vis_data:np.ndarray, invis_data:np.ndarray=None)->None:
#if invis_data is None, then use baum-welch algrithm, if invis_data is given, then use ordinary probability calculation
if invis_data is None:#use bw automatically
pass
else:
if np.shape(vis_data) != np.shape(invis_data):
print("[-] length of two chains are not equal");return
else:
data_len = np.shape(vis_data)[1]
data_num = np.shape(vis_data)[0]
self.vis_kind = vis_data.max() + 1
self.invis_kind = invis_data.max() + 1
# to fill the initial state matrix
self.init_state_mat = np.zeros((self.invis_kind,), dtype=np.float64)
for i in range(data_num):
self.init_state_mat[invis_data[i, 0]] += 1#only the head of one chain
self.init_state_mat /= np.linalg.norm(self.init_state_mat, ord=1)
if self.debug : print(self.init_state_mat)
# to fill the state transfer matrix
self.trans_state_mat = np.zeros((self.invis_kind, self.invis_kind), dtype=np.float64)
for k in range(data_num):
for i in range(data_len - 1):
self.trans_state_mat[invis_data[k, i], invis_data[k, i + 1]] += 1
for i in range(self.invis_kind):
self.trans_state_mat[i] /= np.linalg.norm(self.trans_state_mat[i], ord=1)
if self.debug:print(self.trans_state_mat)
# to fill the emitter matrix
self.emitter_mat = np.zeros((self.invis_kind, self.vis_kind), dtype=np.float64)
for k in range(data_num):
for i in range(data_len):
self.emitter_mat[invis_data[k, i],vis_data[k, i]] += 1
for i in range(self.invis_kind):
self.emitter_mat[i] /= np.linalg.norm(self.emitter_mat[i], ord=1)
if self.debug:print(self.emitter_mat)
#get the specific probability from a known visible chain, with the params of the model known
def get_prob(self, vis_data:np.ndarray, algorithm:str="forward")->float:
'''algorithm : 'traversal' / 'forward' / 'backward'
'''
vis_data = vis_data.ravel()
if self.emitter_mat is None or self.trans_state_mat is None:
print("[-] params have not been infered yet"); return
probability = 0.
if algorithm == 'forward':
data_infer_len = vis_data.shape[0]
prob_data_arr = np.zeros((self.invis_kind, data_infer_len), dtype=np.float64)
#first col of prob
for j in range(self.invis_kind):
prob_data_arr[j, 0] = self.init_state_mat[j] * self.emitter_mat[j, vis_data[0]]
#total time complexity : O(T*N^2)
for i in range(1, data_infer_len):
#calculate this matrix of probability forward
#time complexity : O(N^2)
for j in range(self.invis_kind):# indicator for forward invis nodes
prob_back_node = 0.
for k in range(self.invis_kind):# indicator for last(back) invis nodes
prob_back_node += prob_data_arr[k, i-1] * self.trans_state_mat[k, j] * self.emitter_mat[j, vis_data[i]]
prob_data_arr[j, i] = prob_back_node
if self.debug:print(prob_data_arr)
probability = prob_data_arr[:, -1].sum()
if self.debug:print(probability)
elif algorithm == 'backward':
data_infer_len = vis_data.shape[0]
prob_data_arr = np.zeros((self.invis_kind, data_infer_len+1), dtype=np.float64)
#last col of the prob
for j in range(self.vis_kind):
prob_data_arr[j, -1] = 1
#total time complexity : O(T*N^2)
for i in range(data_infer_len - 1, -1, -1):
#calculate this matrix of probability backward
#time complexity : O(N^2)
for j in range(self.invis_kind):#indicator for backward invis nodes
prob_front_node = 0.
for k in range(self.invis_kind):#indicator for last(front) invis nodes
prob_front_node += prob_data_arr[k, i+1] * self.trans_state_mat[j, k] * self.emitter_mat[j, vis_data[i]];
prob_data_arr[j, i] = prob_front_node
for j in range (self.vis_kind):
probability += prob_data_arr[j, 0] * self.init_state_mat[j]
if self.debug:print(prob_data_arr)
elif algorithm == 'traversal':
invis_data = np.zeros(vis_data.shape, dtype=np.int)
#generate all possible invisible sequences, with traversing method
data_infer_len = vis_data.shape[0]
for i in range(self.invis_kind**data_infer_len-1):
probability_this_chain = 1.
#calculate the probability of this very sequence and add it to total probability
for k in range(data_infer_len):
# P(vis_data[k]|invis_data[k])
# not bayes law type, reason invis -> result vis : regard invis as reason
probability_this_chain *= self.emitter_mat[invis_data[k], vis_data[k]]
for k in range(0, data_infer_len - 1):
# P(invis_data[k]->invis_data[k+1])
probability_this_chain *= self.trans_state_mat[invis_data[k], invis_data[k+1]]
probability_this_chain *= self.init_state_mat[invis_data[0]]
# if self.debug : print(probability_this_chain)
probability += probability_this_chain
#update the chain
invis_data[0] += 1
for j in range(data_infer_len - 1):
if invis_data[j] == self.invis_kind:
invis_data[j] = 0
invis_data[j+1] += 1
if self.debug : print(probability)
else:
print("[-] should choose the right algorithm");return
return probability
def get_hidden(self, vis_data:np.ndarray, algorithm:str="Viterbi")->np.ndarray:
'''algorithm : 'Viterbi"
'''
if algorithm == "Viterbi":
pass
else:
print("[-] should choose the right algorithm");return
类似的数据集很少，因此本人自制了一个生成隐马尔可夫链的程序。还可以根据生成时的原始参数检验各种算法的正确性。
#data_gen.py
#this file is used to generate original data for hmm training
import numpy as np
#suppose 3 invis state, 3 vis state
chain_len = 100
chain_num = 500
#initial invisible state probability
# prob 0 1 2
# p p p
init_state_prob = np.array([0.3, 0.2, 0.5])
#here we assume this to be not equal
#invisible state transfer matrix
# past\cur 0 1 2
# 0 p p p
# 1 p p p
# 2 p p p
trans_state_mat = np.array([
[0.2, 0.4, 0.4],
[0.4, 0.4, 0.2],
[0.3, 0.3, 0.4]
])
#invisible state -> visible state matrix
# invis\vis 0 1 2
# 0 p p p
# 1 p p p
# 2 p p p
emitter_mat = np.array([
[0.3, 0.4, 0.3],
[0.5, 0.3, 0.2],
[0.2, 0.5, 0.3]
])
def get_chain()->tuple([np.ndarray, np.ndarray]):
vis_chains = np.ndarray((chain_num, chain_len), dtype=np.int)
invis_chains = np.ndarray((chain_num, chain_len), dtype=np.int)
for i in range(chain_num):
#generate invisible chain
start_code = np.random.random()
invis_chain = list()
if start_code < init_state_prob[0]:
start_invis_state = np.array([1., 0., 0.])
invis_chain.append(0)
elif start_code < init_state_prob[1] + init_state_prob[0]:
start_invis_state = np.array([0., 1., 0.])
invis_chain.append(1)
else:
start_invis_state = np.array([0., 0., 1.])
invis_chain.append(2)
invis_state = start_invis_state
while len(invis_chain) < chain_len:
next_state_prob = (invis_state @ trans_state_mat)
next_code = np.random.random()
if next_code < next_state_prob[0]:
invis_state = np.array([1., 0., 0.])
invis_chain.append(0)
elif next_code < next_state_prob[0] + next_state_prob[1]:
invis_state = np.array([0., 1., 0.])
invis_chain.append(1)
else:
invis_state = np.array([0., 0., 1.])
invis_chain.append(2)
#generate visible chain
vis_chain = list()
for invis_state_code in invis_chain:
if invis_state_code == 0:
invis_state = np.array([1., 0., 0.])
elif invis_state_code == 1:
invis_state = np.array([0., 1., 0.])
else:
invis_state = np.array([0., 0., 1.])
vis_state_prob = invis_state @ emitter_mat
vis_code = np.random.random()
if vis_code < vis_state_prob[0]:
vis_chain.append(0)
elif vis_code < vis_state_prob[0] + vis_state_prob[1]:
vis_chain.append(1)
else:
vis_chain.append(2)
vis_chains[i, :] = vis_chain
invis_chains[i, :] = invis_chain
return vis_chains, invis_chains
编写代码产生对象进行测试
#main.py
import numpy as np
from data_gen import get_chain
import data_gen
from hmm import discrete_hidden_Markov_model
#initialize
yyz_discrete_HMM_machine = discrete_hidden_Markov_model(debug=False)
# strict test
# yyz_discrete_HMM_machine.emitter_mat = data_gen.emitter_mat
# yyz_discrete_HMM_machine.trans_state_mat = data_gen.trans_state_mat
# yyz_discrete_HMM_machine.init_state_mat = data_gen.init_state_prob
# yyz_discrete_HMM_machine.invis_kind = 3
# yyz_discrete_HMM_machine.vis_kind = 3
#fit test
vis, invis = get_chain()
yyz_discrete_HMM_machine.fit(vis, invis)
#print params
print(yyz_discrete_HMM_machine.emitter_mat, yyz_discrete_HMM_machine.trans_state_mat, yyz_discrete_HMM_machine.init_state_mat)
#normalization test : total probability is 1.
data_infer_len = 6
vis_data = np.zeros((data_infer_len,), dtype=np.int)
# generate all possible invisible sequences, with traversing method
prob_for = 0.
prob_tra = 0.
prob_bak = 0.
for i in range(3**data_infer_len):
prob_tra += yyz_discrete_HMM_machine.get_prob(vis_data, algorithm='traversal')
prob_bak += yyz_discrete_HMM_machine.get_prob(vis_data, algorithm='backward')
prob_for += yyz_discrete_HMM_machine.get_prob(vis_data, algorithm='forward')
vis_data[0] += 1
for j in range(data_infer_len - 1):
if vis_data[j] == 3:
vis_data[j] = 0
vis_data[j+1] += 1
print(prob_for, prob_tra, prob_bak)
#result
拟合结果
发射矩阵
[[0.30223322 0.3989192 0.29884758]
[0.50214004 0.29603819 0.20182177]
[0.20046293 0.49771578 0.30182128]]
状态转移矩阵
[[0.20398501 0.4028408 0.3931742 ]
[0.39799201 0.39865764 0.20335034]
[0.30328927 0.29505072 0.40166001]]
初始概率
[0.298 0.224 0.478]
归一化结果
1.0 0.9950028676787088 0.9999999999999998
得到的概率矩阵和生成代码时在误差允许范围内相等，说明本初级统计型拟合程序有效；三种算法都具有归一化的特性，典型功能2算法测试成功。
总结
- 对隐马尔可夫模型做了简要介绍
- 由于算法之间的加法、乘法方式和次数不同，理论上结果应当相同的算法之间也产生了偏差。这是数据结构的精度所导致的。
- 今天是2.11除夕夜，这一篇其实写了挺久的，主要这会儿看春晚太无聊就写一下总结。另外，祝各位网友牛年新年快乐！
